Atomistry » Zinc » PDB 1hxy-1i95 » 1hzx
Atomistry »
  Zinc »
    PDB 1hxy-1i95 »
      1hzx »

Zinc in PDB 1hzx: Crystal Structure of Bovine Rhodopsin

Protein crystallography data

The structure of Crystal Structure of Bovine Rhodopsin, PDB code: 1hzx was solved by D.C.Teller, T.Okada, C.A.Behnke, K.Palczewski, R.E.Stenkamp, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.80
Space group P 41
Cell size a, b, c (Å), α, β, γ (°) 97.246, 97.246, 149.544, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 21.2

Other elements in 1hzx:

The structure of Crystal Structure of Bovine Rhodopsin also contains other interesting chemical elements:

Mercury (Hg) 6 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Bovine Rhodopsin (pdb code 1hzx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of Bovine Rhodopsin, PDB code: 1hzx:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 1hzx

Go back to Zinc Binding Sites List in 1hzx
Zinc binding site 1 out of 7 in the Crystal Structure of Bovine Rhodopsin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Bovine Rhodopsin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn957

b:65.0
occ:0.50
NE2 A:GLN279 2.0 45.2 1.0
OE2 A:GLU201 2.1 51.9 1.0
CD A:GLN279 2.7 45.8 1.0
OE1 A:GLN279 2.9 47.5 1.0
CD A:GLU201 3.0 50.8 1.0
CG A:GLU201 3.3 49.0 1.0
CE1 A:PHE276 3.7 34.6 1.0
O A:PHE276 3.9 44.9 1.0
CG A:GLN279 4.1 44.6 1.0
CD1 A:PHE276 4.1 36.1 1.0
OE1 A:GLU201 4.2 51.1 1.0
CZ A:PHE276 4.4 32.9 1.0
CA A:PRO194 4.6 39.5 1.0
CB A:GLU201 4.7 48.7 1.0
CG A:PRO194 4.7 38.8 1.0
CB A:PRO194 4.8 38.3 1.0
O A:TYR191 4.8 36.6 1.0
N A:PRO194 5.0 38.7 1.0
C A:PHE276 5.0 43.5 1.0

Zinc binding site 2 out of 7 in 1hzx

Go back to Zinc Binding Sites List in 1hzx
Zinc binding site 2 out of 7 in the Crystal Structure of Bovine Rhodopsin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Bovine Rhodopsin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn959

b:39.5
occ:1.00
CA A:GLY329 2.6 74.4 1.0
NZ A:LYS311 3.0 41.6 1.0
CE1 B:HIS100 3.2 36.0 1.0
NH2 A:ARG314 3.3 30.5 1.0
N A:GLY329 3.5 72.4 1.0
NE2 B:HIS100 3.5 37.2 1.0
N A:ASP330 3.5 76.3 1.0
C A:GLY329 3.5 75.8 1.0
ND2 A:ASN315 3.6 42.5 1.0
CE A:LYS311 3.8 42.9 1.0
NE A:ARG314 3.8 30.4 1.0
O A:LEU328 3.9 69.2 1.0
CZ A:ARG314 4.0 28.7 1.0
C A:LEU328 4.0 71.1 1.0
OD1 A:ASN315 4.0 42.8 1.0
CG A:ASN315 4.2 41.7 1.0
O A:PRO327 4.3 73.0 1.0
ND1 B:HIS100 4.3 34.1 1.0
CG A:LYS311 4.4 43.4 1.0
OH B:TYR96 4.4 66.4 1.0
O A:GLY329 4.7 76.5 1.0
CD A:LYS311 4.7 43.6 1.0
CE2 B:TYR96 4.7 60.4 1.0
CZ B:TYR96 4.8 63.3 1.0
CD2 B:HIS100 4.8 36.5 1.0
CA A:ASP330 4.9 76.0 1.0

Zinc binding site 3 out of 7 in 1hzx

Go back to Zinc Binding Sites List in 1hzx
Zinc binding site 3 out of 7 in the Crystal Structure of Bovine Rhodopsin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Bovine Rhodopsin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn962

b:47.8
occ:0.50
ND1 A:HIS211 2.2 35.3 1.0
O A:MET163 2.6 28.7 1.0
NE1 A:TRP126 2.7 35.4 1.0
CE1 A:HIS211 2.7 36.2 1.0
CB A:CYS167 2.7 25.3 1.0
OE1 A:GLU122 2.9 30.9 1.0
CG A:HIS211 3.1 34.9 1.0
CD A:GLU122 3.3 31.6 1.0
CG A:GLU122 3.3 31.8 1.0
C A:MET163 3.4 29.0 1.0
CD1 A:TRP126 3.5 34.5 1.0
NE2 A:HIS211 3.6 36.0 1.0
CA A:ALA164 3.6 27.2 1.0
CB A:GLU122 3.6 29.7 1.0
N A:CYS167 3.7 27.8 1.0
O A:ALA164 3.8 23.5 1.0
CB A:HIS211 3.8 34.8 1.0
CE2 A:TRP126 3.8 35.2 1.0
CA A:CYS167 3.8 25.8 1.0
CD2 A:HIS211 3.8 35.9 1.0
N A:ALA164 3.8 28.3 1.0
SG A:CYS167 3.9 25.3 1.0
C A:ALA164 4.0 25.6 1.0
CZ2 A:TRP126 4.2 34.5 1.0
OE2 A:GLU122 4.3 32.5 1.0
CA A:MET163 4.5 30.6 1.0
CA A:HIS211 4.7 34.4 1.0
C A:ALA166 4.7 28.8 1.0
CB A:MET163 4.7 32.7 1.0
CG A:TRP126 4.8 32.3 1.0
CA A:GLU122 4.9 27.8 1.0
CB A:ALA164 4.9 29.2 1.0
C A:CYS167 4.9 25.1 1.0
CD2 A:TRP126 4.9 33.8 1.0

Zinc binding site 4 out of 7 in 1hzx

Go back to Zinc Binding Sites List in 1hzx
Zinc binding site 4 out of 7 in the Crystal Structure of Bovine Rhodopsin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Bovine Rhodopsin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn964

b:46.9
occ:0.50
CG A:PRO267 2.3 24.4 1.0
N A:TYR268 2.5 31.3 1.0
CB A:TYR268 3.1 32.6 1.0
CD A:PRO267 3.1 22.8 1.0
CB A:PRO267 3.2 24.9 1.0
CA A:TYR268 3.3 31.6 1.0
O A:CYS264 3.3 24.8 1.0
O A:PRO291 3.3 15.1 1.0
C A:PRO267 3.4 29.1 1.0
N A:PRO267 3.6 23.5 1.0
CA A:PRO267 3.6 26.1 1.0
C A:CYS264 3.8 24.0 1.0
C A:TRP265 3.8 22.7 1.0
CB A:PRO291 3.8 13.6 1.0
CA A:TRP265 3.9 22.2 1.0
O A:TRP265 3.9 22.3 1.0
C A:PRO291 4.0 15.0 1.0
CA A:PRO291 4.0 14.2 1.0
CD2 A:PHE294 4.0 18.9 1.0
N A:TRP265 4.1 22.7 1.0
CB A:ALA295 4.2 15.8 1.0
O A:ILE263 4.3 25.2 1.0
C A:LEU266 4.4 22.4 1.0
N A:LEU266 4.4 23.0 1.0
CE2 A:PHE294 4.4 17.1 1.0
O A:PRO267 4.4 29.7 1.0
CG A:TYR268 4.5 33.0 1.0
C A:TYR268 4.6 30.3 1.0
CA A:ALA295 4.7 18.5 1.0
N A:ALA295 4.8 17.8 1.0
CA A:CYS264 4.8 24.3 1.0
N A:ALA269 4.9 30.2 1.0

Zinc binding site 5 out of 7 in 1hzx

Go back to Zinc Binding Sites List in 1hzx
Zinc binding site 5 out of 7 in the Crystal Structure of Bovine Rhodopsin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Bovine Rhodopsin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn956

b:65.2
occ:0.50
NE2 B:HIS195 3.0 56.9 1.0
O B:PRO7 3.0 42.9 1.0
CE1 B:HIS195 3.6 56.4 1.0
CB B:PRO7 3.7 37.6 1.0
CA B:PRO7 3.7 38.4 1.0
C B:PRO7 3.7 40.6 1.0
CD2 B:HIS195 4.1 57.7 1.0
OE1 B:GLU197 4.2 70.3 1.0
NH2 B:ARG177 4.7 32.2 1.0
ND1 B:HIS195 4.7 55.9 1.0
CD B:GLU197 4.7 69.6 1.0
OE2 B:GLU197 4.9 70.2 1.0

Zinc binding site 6 out of 7 in 1hzx

Go back to Zinc Binding Sites List in 1hzx
Zinc binding site 6 out of 7 in the Crystal Structure of Bovine Rhodopsin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Bovine Rhodopsin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn958

b:65.2
occ:0.40
NE2 B:GLN279 1.6 49.4 1.0
OE2 B:GLU201 2.5 79.0 1.0
CD B:GLN279 2.7 46.9 1.0
OE1 B:GLN279 3.1 45.6 1.0
CD B:GLU201 3.5 77.0 1.0
O B:PHE276 3.9 33.0 1.0
CG B:GLU201 3.9 74.1 1.0
CG B:GLN279 4.0 46.0 1.0
CG B:PRO194 4.4 51.1 1.0
CE1 B:PHE276 4.5 32.4 1.0
OE1 B:GLU201 4.5 78.5 1.0
CB B:PRO194 4.7 51.5 1.0
CD1 B:PHE276 4.8 31.4 1.0
CA B:PRO194 4.8 50.1 1.0
CB B:GLN279 4.9 45.8 1.0

Zinc binding site 7 out of 7 in 1hzx

Go back to Zinc Binding Sites List in 1hzx
Zinc binding site 7 out of 7 in the Crystal Structure of Bovine Rhodopsin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Bovine Rhodopsin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn963

b:53.8
occ:0.50
ND1 B:HIS211 2.2 45.8 1.0
NE1 B:TRP126 2.5 55.8 1.0
O B:MET163 2.6 49.8 1.0
CE1 B:HIS211 2.6 46.5 1.0
CB B:CYS167 2.8 43.9 1.0
OE1 B:GLU122 3.0 43.2 1.0
CG B:HIS211 3.1 45.3 1.0
C B:MET163 3.3 48.2 1.0
CD1 B:TRP126 3.4 55.3 1.0
CD B:GLU122 3.5 43.0 1.0
CG B:GLU122 3.5 40.6 1.0
NE2 B:HIS211 3.6 46.5 1.0
CE2 B:TRP126 3.6 56.2 1.0
CA B:ALA164 3.6 43.9 1.0
CB B:GLU122 3.7 38.1 1.0
CB B:HIS211 3.7 44.1 1.0
CD2 B:HIS211 3.8 46.8 1.0
N B:ALA164 3.8 46.2 1.0
N B:CYS167 3.8 43.8 1.0
O B:ALA164 3.9 41.7 1.0
CA B:CYS167 3.9 43.0 1.0
SG B:CYS167 4.1 45.7 1.0
CZ2 B:TRP126 4.1 57.1 1.0
C B:ALA164 4.1 42.3 1.0
CA B:MET163 4.4 48.5 1.0
OE2 B:GLU122 4.4 43.9 1.0
CB B:MET163 4.6 50.1 1.0
CG B:TRP126 4.6 53.6 1.0
CA B:HIS211 4.6 43.4 1.0
CD2 B:TRP126 4.7 55.3 1.0
C B:ALA166 4.8 43.7 1.0
CB B:ALA164 4.9 43.2 1.0
CA B:GLU122 4.9 36.1 1.0
CB B:ALA166 5.0 42.4 1.0

Reference:

D.C.Teller, T.Okada, C.A.Behnke, K.Palczewski, R.E.Stenkamp. Advances in Determination of A High-Resolution Three-Dimensional Structure of Rhodopsin, A Model of G-Protein-Coupled Receptors (Gpcrs). Biochemistry V. 40 7761 2001.
ISSN: ISSN 0006-2960
PubMed: 11425302
DOI: 10.1021/BI0155091
Page generated: Wed Dec 16 02:52:10 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy